The genetic heritage of Alpine local cattle breeds using genomic SNP data

Abstract

Background: Assessment of genetic diversity and population structure provides important control metrics to avoid genetic erosion, inbreeding depression and crossbreeding between exotic and locally-adapted cattle breeds since these events can have deleterious consequences and eventually lead to extinction. Historically, the Alpine Arc represents an important pocket of cattle biodiversity with a large number of autochthonous breeds that provide a fundamental source of income for the entire regional economy. By using genotype data from medium-density single nucleotide polymorphism (SNP) arrays, we performed a genome-wide comparative study of 23 cattle populations from the Alpine Arc and three cosmopolitan breeds. Results: After filtering, we obtained a final genotyping dataset consisting of 30,176 SNPs for 711 individuals. The local breeds showed high or intermediate values of genetic diversity compared to the highly selected cosmopolitan breeds. Patterns of genetic differentiation, multidimensional scaling, admixture analysis and the constructed phylogenetic tree showed convergence, which indicates the presence of gene flow among the breeds according to both geographic origin and historical background. Among the most differentiated breeds, we identified the modern Brown cattle. In spite of admixture events, several local breeds have preserved distinctive characteristics, which is probably due to differences in genetic origin and geographic location. Conclusions: This study represents one of the most comprehensive genome-wide analysis of the Alpine cattle breeds to date. Using such a large dataset that includes the majority of the local breeds found in this region, allowed us to expand knowledge on the evaluation and status of Alpine cattle biodiversity. Our results indicate that although many of the analyzed local breeds are listed as endangered, they still harbor a large amount of genetic diversity, even when compared to some cosmopolitan breeds. This finding, together with the reconstruction of the phylogeny and the relationships between these Alpine Arc cattle breeds, provide crucial insights not only into the improvement of genetic stocks but also into the implementation of future conservation strategies.

Refining the genetic structure and relationships of European cattle breeds through meta-analysis of worldwide genomic SNP data, focusing on Italian cattle

“…We also noted the outlier behavior of some Italian breeds, such as that of Burlina cattle. Neighbor-Net and MDS analysis separated this breed from the Northern Italian cluster owing to admixture events with Italian Holstein cattle 17 , 34 . Finnish Ayrshire, Norwegian Red, and Kholmogory were the European breeds closest to Burlina cattle and the breeds that were likely to have been influenced by the Holstein genetic component.…”

“…For analyses of comparative population genomics, SNP genotyping data from previously published 7 , 10 , 12 , 15 – 17 , 21 , 24 work were merged with PLINK 34 . Spanish breeds (Terrana, Asturiana, Pasiega, and Tudanca) were genotyped for this study.…”

Genome‐wide assessment of diversity and differentiation between original and modern Brown cattle populations

“…2017; Senczuk et al . 2020b), but to the best of our knowledge, this is the first study on the identification of differentiated genomic regions between original and modern Brown cattle populations.…”

“…2017; Senczuk et al . 2020b). The observed genetic differentiation among breeds was in accordance with their geographical and historical origins.…”

Genetic diversity and population history of eight Italian beef cattle breeds using measures of autozygosity

“…Assessment of genetic diversity and population structure is an important task to understand the evolutionary history of the breeds, but also to provide important information for the conservation and management of biodiversity [20]. Italy has a biodiversity reservoir for local breeds, but generally, local populations have a small sample size and one of the most important obstacle is the increase in inbreeding, leading to negative effect on production and reproduction traits [21].…”